Of course, supporting saving to a compressed format would be stupid, but there's lots of compressed QB files out there. Remember that QB64's aim is to be compatible with QBASIC & QB4.5, so being able to load the compressed QB4.5 format is desirable.
Heck, you could even write the decoder in QB64 as a function and I'll add it into the QB64 IDE/compiler. Fact is though this is a low priority for QB64 development so at this stage someone else would have to do this instead of me.